In March 2015, Marshall announced she was taking a leave of absence for health-related reasons. A subsequent inquiry by Willamette Week found she had been suspended by the United States Department of Justice (DOJ) pending investigation she had been in a romantic relationship with a co-worker. Media reports in The Oregonian and Willamette Week claimed that Marshall had been sending numerous text messages and emails to a federal prosecutor under police protection due to threats against his life from the Mexican Mafia. The reports also incorrectly alleged Marshall had been following the prosecutor and his bodyguards outside of working hours.[11] The U.S. Department of Justice later released the full report from the investigation indicated that news reports from Willamette Week were misleading and that Marshall had had an affair with a subordinate in an on again off again nature for over a year.
According to Willamette Week, the incidents had been an open secret in Portland, Oregon, for some time; its discovery by DOJ officials in Washington, D.C., prompted the suspension of Marshall and revocation of her security clearance. The following month, Marshall resigned citing unspecified health issues. According to Marshall, she had been receiving treatment for her unspecified health issues but "it was not sufficient."[12][13]

In March 2018 the Oregon Bar Association and former U.S. Attorney Amanda Marshall reached an agreement in which her law license was suspended for 90 days followed by 2 years of probation for lying to investigators during the investigation of the misconduct charges against her. During her probation Marshall agreed to see a mental health care professional.[14]

^Nigel Jaquiss (March 18, 2015). "Fatal Attraction Fallout". Willamette Week. Retrieved April 25, 2015. Marshall, who is married to Yamhill County Circuit Judge Ladd Wiles and commutes to Portland from McMinnville, had talked about pursuing the CEO's job at SAIF Corp., the state-owned workers compensation insurer, and interviewed with at least one private law firm.